diff sixgill_makefasta.xml @ 0:cf8eee8343fb draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sixgill_makefasta.xml	Thu Oct 13 08:38:04 2016 -0400
@@ -0,0 +1,76 @@
+<tool id="sixgill_makefasta" name="sixgill makefasta" version="@VERSION@.0">
+    <description>from a metapeptide database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <version_command>sixgill_makefasta --version</version_command>
+    <command><![CDATA[
+        sixgill_makefasta 
+            --out=metapeptides_fa_output.fa
+            --type="$fa_type.fasta_type"
+            #if $fa_type.fasta_type == 'peptide':
+                --missedcleavages=$fa_type.missedcleavages
+                --minpeptidelength=$fa_type.minpeptidelength
+            #end if
+            "$metapeptide_db"
+    ]]></command>
+    <inputs>
+        <param name="metapeptide_db" type="data" format="tabular" label="metapeptide database" 
+         help="Can be generated with sixgill_build"/>
+        <conditional name="fa_type">
+            <param name="fasta_type" type="select" label="fasta type">
+                <help> peptide with specified missed cleavages requires holding
+                       all peptides in the database in memory, as each is only written once
+                </help>
+                <option value="aa" selected="true">aa - amino acid</option>
+                <option value="peptide">peptide - with specified missed cleavages</option>
+            </param>
+            <when value="aa"/>
+            <when value="peptide">
+                <param name="missedcleavages" type="integer" value="0" min="0" max="6" label="missedcleavages"/>
+                <param name="minpeptidelength" type="integer" value="7" min="1" label="minpeptidelength"/>
+            </when>
+        </conditional>
+        
+    </inputs>
+    <outputs>
+        <data name="output_fa" format="fasta" label="${tool.name} on ${on_string}: metapeptide.fa" from_work_dir="metapeptides_fa_output.fa"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="metapeptide_db" ftype="tabular" value="testdb_metagene.metapeptides.tsv"/>
+            <param name="fasta_type" value="aa"/>
+            <output name="output_fa">
+                <assert_contents>
+                    <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+usage: sixgill_makefasta [-h] --out OUT --type {aa,peptide}
+                         [--missedcleavages MISSEDCLEAVAGES]
+                         [--minpeptidelength MINPEPTIDELENGTH] [--debug]
+                         metapeptidedbfile
+
+Build a fasta database from a metapeptide database. Either nucleotide or amino
+acid.
+
+positional arguments:
+  metapeptidedbfile     input metapeptide database file
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --out OUT             output file
+  --type {aa,peptide}   database type
+  --missedcleavages MISSEDCLEAVAGES
+                        missed cleavages (for type peptide only)
+  --minpeptidelength MINPEPTIDELENGTH
+                        minimum peptide length (for type peptide only)
+  --debug               Enable debug logging
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>